To start with addressing the premise of your question, it's probably wrong to say that pre-modern people were much shorter than modern people. Here is a good image of data from this study (PDF) that shows that male skeletal remains from the past 2000 years in northern Europe remained around 170cm (or 5'6.9") until they spiked to around 180cm today. The average height of an American male is 177cm (or 5'9.7"). So really we're talking about a difference of 3-4 inches.

The persistent myth that people were significantly smaller than that historically relies on overconfidence in the role nutrition plays in growth (height is mostly [EDIT roughly 60-80%] genetic) and often comes from mistaken interpretations of doorways (which were small because they were structural weak points) and furniture (which wasn't that small, but was often smaller due to expense).

As for penis and breast size, it's hard to say empirically because soft tissue doesn't preserve well. However, penis and breast growth aren't as dependent on long term nutrition as skeletal growth is. Breast size in particular fluctuates quite a lot throughout a woman's lifetime. Puberty, pregnancy, breastfeeding, weight gain or loss, and more can all play a role. And the penis does most of its growing during puberty, so childhood nutrition would be less of a factor than it is for skeletal growth.

Basically, the best answer is that maybe penises and breasts were a bit smaller, but it's unlikely that the difference was as big as the difference in adult heights. But it's not likely to be that significant, especially as adults weren't even that much shorter throughout history.

EDIT: In my original answer I may have mistakenly implied that nutrition plays little to no role in determining adult height. In fact, it is very significant. Certainly the second most significant factor, after genetics. My point was that nutrition doesn't make as big a difference as people tend to think. Basically, if you are genetically predetermined to a height range of 5'5" to 5'7", no amount of nutritional help will get you to 6', and no amount of starving will keep you much below 5' without killing you (although a secondary disease like rickets or pituitary disorders could).